The effect of mechanical pre-treatment of nine different agricultural substrates minced to particle sizes of 1.5 mm, 5 mm and 10 mm on biogas and methane yields and fermentation kinetics was investigated. The results showed, that for five of the nine tested substrates (grass, Progas rye, Palazzo rye, tall wheatgrass, beet), a higher biogas production was obtained for the degree of fragmentation of 10 mm compared to fragmentation of 5 mm and 1.5 mm. For fragmentation of 5 mm, the highest biogas production was achieved for sorghum silage, Atletico maize and Cannavaro maize—649.80, 735.59 and 671.83 Nm3/Mg VS, respectively. However, for the degree of fragmentation of 1.5 mm, the highest biogas production (510.43 Nm3/Mg volatile solid (VS)) was obtained with Topinambur silage. The modified Gompertz model fitted well the kinetics of anaerobic digestion of substrates and show a significant dependence of the model parameters Hmax (biogas production potential) and Rmax (maximum rate of biogas production) on the degree of substrate fragmentation.